This Week in Genome Biology

Early stage breast neoplasias tend to share transcriptional traits with one another, according to a study in the early edition of Genome Biology.

Researchers from Stanford University and the University of Notre Dame did RNA sequencing on formalin-fixed, paraffin-embedded breast neoplasia sample from 25 individuals and on breast cancer and normal tissues from the same patients. Although gene expression patterns in the neoplasias were distinct from those in corresponding tumor and normal samples, investigators found that the group of pre-cancerous lesions shared certain patterns independent of their underlying genetics or future clinical features. In particular, the neoplasias showed enhanced ERBB2, FOXA1, and GATA3 gene expression ? a pattern the team verified by testing even earlier breast neoplasia samples.

Australian researchers report on factors contributing to the inheritance of DNA methylation patterns across multiple generations. The team performed array-based cytosine methylation profiling on peripheral white blood cells from 614 individuals representing 117 multi-generational families. From the heritability estimates and methylation marks detected in these families, the group determined that most transgenerational methylation inheritance can be traced back to genetic determinants and mainly involves so-called CpG sites in the genome, where cytosine and guanine bases frequently occur together.

An international team led by investigators in Canada and France used genomic and transcriptomic profiling to take a look at genome architecture in the polyploid model plant Brassica oleracea. Using a combination of Illumina and Roche 454 sequencing approaches, the researchers put together a B. oleracea genome assembly that's believed to cover some 75 percent of the plant's total genome sequence. By adding in leaf transcriptome and methylome information, they were able to start characterizing gene function, dominance, and evolutionary patterns across the polyploid plant's sub-genomes.